Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,560,455	+G	intergenic (+589/+167)	rtcR → / ← glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,560,455	1	.	G	94.1%	46.0 / ‑2.9	17	intergenic (+589/+167)	rtcR/glpG	DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (9/7);  total (10/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.32e-01

CCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTG  >  NC_000913/3560216‑3560695                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                  ccATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCCGTGATTGAGCAGTGGGTGGGCTACCGCTTCCGGGGTGGTGCCGATATCGATAAACAGCGTCGAGCCCTTGGGGATTTGCACCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTCGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCC‑GGATCAgg                                                                                                                                                                                                                                        >  1:291935/1‑251 (MQ=255)                                      aaTGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGTTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTGGAGCCATTGGGGATTTGCTCCGCCCCTTTGGGGGTGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGAGGGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAg                                                                                                                                                                                                   <  1:308243/251‑1 (MQ=255)                                           gcAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCAGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGTCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGCTCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAg                                                                                                                                                                                                   >  1:325929/1‑246 (MQ=255)                                                ttGCTGTGATTGAGCAGTGCGTGCGCTCCCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGACCCATGGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGTGAATAGTCTGCGGGc                                                                                                                                                                                          <  1:189865/250‑1 (MQ=255)                                                       gATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACgg                                                                                                                                                                                    >  1:71969/1‑249 (MQ=255)                                                              cAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGCTGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCCCCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                                                                                                                           >  1:151600/1‑251 (MQ=255)                                                                            ccGCTTCCGGCGGGGTGCCGATATCGATAA‑CAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCTGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgn                                                                                                                                                            <  1:79554/251‑2 (MQ=255)                                                                                    ggcgggggtccgattgcGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCTCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GTATCAGGTTTGGCGCCGCCAGCTCATTGAGGTCTCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGan                                                                                                                                                     <  1:37763/235‑2 (MQ=255)                                                                                                                            ggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGNTCCNNNNNCtnnnnnnnnnn                                                                                                                                                                                                              >  2:198054/1‑144 (MQ=255)                                                                                                                               tngccncnncnntttnGCGGGGGTTGCGCTTTTTTTTNNGGGTCGGGGNGGCCTGGGGTTCGGGCCACGGGGTGTTACCCGAACTGGAGGGCAGCGCCGCACNGCCATGATGNNGCN‑GGATCNGNNNTNNNTCNGCCAGCTCATTGAGGTCGCNGCNNATAGTCNGCGGGCTGACGGAGAAATGCTCTAcc                                                                                                                                                                      <  2:71969/178‑1 (MQ=255)                                                                                                                                                     gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCCGCTCATTGAGGTCGCGGCGACTAGTCTGCGGGTTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATAcc                                                                                                                    >  1:320365/1‑219 (MQ=255)                                                                                                                                                               ttttCTGCGGTCTGGGTGGCCTTGCGTGCGTGCCCCGGCGTGTTAACCTAACGGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTggn                                                                             <  1:198054/248‑2 (MQ=255)                                                                                                                                                                        gTCTGGGTGGCCTTGCGATCGTGCCACGGCGTATTAACCGAACTGGAAGGCCGCGCCCCACCGCCATGATGGCGCC‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATCGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAAcc                                                                                                                                  >  1:128965/1‑186 (MQ=255)                                                                                                                                                                                 gCCTTGCGATCGTGCCACGGCGTGTTCACCGACCTGGAAGGCAGCGCCGAACCGCCACGATGGC‑GACGGACCAGGTTTTGCTCCGCCAGCTCATTGCGGTCGAGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCATGGAATTATTTTCGTTTTCGCGCAt                                                        >  1:304222/1‑251 (MQ=255)                                                                                                                                                                                                          tAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTACGCCAGCTCATTGAGGACGCGGCGAATAGTCTGCGGGCTGCCGGAGAAATGATCTCCCAGCTCTTCGGCACTGACATAACCCTGCTGTTTACCCAGTTCGCTAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACACAAGCCATCGc                               >  1:310411/1‑251 (MQ=255)                                                                                                                                                                                                                                     cGCCATGATGGCGCA‑GGATTAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTTTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAAt                                               <  1:271437/208‑1 (MQ=255)                                                                                                                                                                                                                                       ccATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACAAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACACGGCGAtgtgtg  >  1:230742/1‑251 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                  CCATCAACGTGTTAGCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTCATTTATAAATCCCTGGAATTATTTTCGTTTTCGCGCATTGAGCGAATCAACAAAAGCCATCGCTAAACCCACGGCTAACCCGGCGATGTGTG  >  NC_000913/3560216‑3560695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑